3LW0 | pdb_00003lw0

IGF-1RK in complex with ligand MSC1609119A-1

PDB DOI:&nbsphttps://doi.org/10.2210/pdb3LW0/pdb

Classification:&nbspTRANSFERASE
Organism(s):&nbspHomo sapiens
Expression System:&nbspSpodoptera frugiperda
Mutation(s):&nbspYes&nbsp

Deposited:&nbsp2010-02-23&nbspReleased:&nbsp2010-09-29&nbsp
Deposition Author(s):&nbspGraedler, U., Heinrich, T., Boettcher, H., Blaukat, A., Shutes, A., Askew, B.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.79 Å
R-Value Free:&nbsp
0.185 (Depositor), 0.200 (DCC)&nbsp
R-Value Work:&nbsp
0.157 (Depositor), 0.170 (DCC)&nbsp

Starting Model: experimental
View more details

wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 1.3 of the entry. See complete&nbsphistory.&nbsp

Literature

Allosteric IGF-1R Inhibitors.

Heinrich, T.,&nbspGradler, U.,&nbspBottcher, H.,&nbspBlaukat, A.,&nbspShutes, A.

(2010) ACS Med Chem Lett&nbsp1: 199-203

PubMed:&nbsp24900194&nbspSearch on PubMedSearch on PubMed Central
DOI:&nbsphttps://doi.org/10.1021/ml100044h
Primary Citation of Related Structures: &nbsp
3LW0

PubMed Abstract:&nbsp
Targeting allosteric protein sites is a promising approach to interfere selectively with cellular signaling cascades. We have discovered a novel class of allosteric insulin-like growth factor-I receptor (IGF-1R) inhibitors. 3-Cyano-1H-indole-7-carboxylic acid {1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}amide (10) was found with nanomolar biochemical, micromolar, cellular IGF-1R activity and no relevant interference with cellular insulin receptor signaling up to 30 μM. The allosteric binding site was characterized by X-ray crystallographic studies, and the structural information was used to explain the unique mode of action of this new class of inhibitors.

Organizational Affiliation

Merck Serono, Frankfurter Strasse 250, 64293 Darmstadt, Germany.

Macromolecule Content&nbsp

Total Structure Weight: 142.33 kDa&nbsp
Atom Count: 10,929&nbsp
Modeled Residue Count: 1,168&nbsp
Deposited Residue Count: 1,216&nbsp
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor	A, B, C, D	304	Homo sapiens	Mutation(s): 2&nbsp Gene Names:&nbspIGF1R EC:&nbsp2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP08069&nbsp(Homo sapiens) Explore&nbspP08069&nbsp Go to UniProtKB: &nbspP08069
PHAROS: &nbspP08069 GTEx: &nbspENSG00000140443&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08069
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands&nbsp2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CCX Query on CCX Download Ideal Coordinates CCD File&nbsp SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth C] E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	3-cyano-N-{1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}-1H-indole-7-carboxamide C₂₈ H₂₈ N₆ O GVZDPXYOJHKYRC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File&nbsp SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	I [auth B], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain I [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.79 Å
R-Value Free:&nbsp 0.185 (Depositor), 0.200 (DCC)&nbsp
R-Value Work:&nbsp 0.157 (Depositor), 0.170 (DCC)&nbsp

Space Group:&nbspH 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.346	α = 90
b = 189.346	β = 90
c = 115.92	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View&nbspFull Validation Report

Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2010-09-29&nbsp

Deposition Author(s):&nbsp

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-12-25
Changes: Advisory, Database references
Version 1.3: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description